Championship leader Rosberg, who holds a 14-point lead over Hamilton, was 0.486 seconds faster than Sebastian Vettel (Red Bull) and Valtteri Bottas (Williams) in the final session of qualifying at the Hungarian Grand Prix on Saturday.
Yet Hamilton was unable to battle for the leading places on the grid after a fuel leak ensured he was forced out of qualifying for the second successive race.
A delighted Rosberg acknowledged his third pole position in succession would have been even sweeter had his team-mate been able to challenge.
"It's a pity for the team, not a good thing," said Rosberg. "We need to work on that. That's reliability.
"I would prefer to be out there battling with Lewis, that would give me the maximum adrenalin rush.
"Of course, I am very, very happy but it wasn't a gloves-off battle with Lewis. It takes away a bit of the happiness."
Rosberg very nearly suffered an early exit of his own at the start of the final session, as a short rain shower prompted him to skid off at the first corner.
The German was able to control the slide and guide his car to safety before taking advantage of a drying track to gain pole.
With rain forecast on Sunday, the 29-year-old knows a fifth win of the season is far from guaranteed.
"Tomorrow will be a challenging race, especially with the weather coming, so it is all to play for," he added.
"Qualifying three was a really big challenge, the track was changing all time at the beginning. Starting the lap, I was the first one to arrive at the first corner, it was difficult to judge.
"It was very, very wet so I did take it a bit easy and I managed to avoid crashing. It was just massively difficult down there.
"From then on, it was easier as it started drying again. My last lap, it was nice to nail it."